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 New and Future
Developments in Microbial
Biotechnology and
Bioengineering
 New and Future
Developments in Microbial
Biotechnology and
Bioengineering
Sustainable Agriculture: Advances in
microbe-based biostimulants
Edited by

Harikesh Bahadur Singh

Department of Biotechnology, Institute of
Applied Sciences & Humanities, GLA University, Mathura

Anukool Vaishnav
Department of Biotechnology, Institute of
Applied Sciences & Humanities, GLA University, Mathura;
Swiss Excellence Fellow, Agroecology and Environment,
Agroscope (Reckenholz), Zürich, Switzerland
Elsevier
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Typeset by Aptara, New Delhi, India
Contents
Contributors  xv
About the Editors   xxi
Preface  xxiii

1. Plant growth promoting rhizobacteria - Advances and

future prospects 1
Cristine Marie B. Brown, Robert A. Nepomuceno, Julieta A. Anarna,
Marilyn B. Brown
1.1 Introduction 1
1.2 Review literature & recent developments 2
1.3 Conclusion 21
References 22

2. Prospects of beneficial microbes as a natural resource for

sustainable legumes production under changing climate 29
Ayman EL Sabagh, Md.Sohidul Islam, Akbar Hossain, Muhammad
Aamir Iqbal, Muhammad Imran, Ali Raza, Arzu Çiğ, Allah Wasaya,
Tauqeer Ahmad Yasir, Ade Sumiahadi, Khizer Amanet, Muhammad
Mubeen, Singh Kulvir, Ram Swaroop Meena, Habib-ur-Rehman
Athar, Subhan Danish, Muhammad Faheem Adil, Muhammad
Ali Raza, Akihiro Ueda, Liu Liyun, Murat Erman
2.1 Introduction 30
2.2 Potential of symbiotic nitrogen fixation (SNF) 32
2.3 Factors affecting nodule formation and biological nitrogen
fixation (BNF) 33
2.4 Conclusion 46
2.5 Future prospective 46
Acknowledgments 47
References 47

v
vi Contents

3. Trichoderma as biostimulant - a plausible approach to

alleviate abiotic stress for intensive production practices 57
S. Abirami, S. Sree Gayathri, C. Usha
3.1 Introduction 57
3.2 Review of literature 59
3.3 Conclusion 75
References 76

4. Mode of action of different microbial products in plant

growth promotion 85
Nishar Akhtar, Md.Mahtab Rashid, Shahina Perween,
Gagan Kumar, Satyabrata Nanda
4.1 Introduction 85
4.2 Major microbial genera and their products 87
4.3 Mode of action(s) of microbes and their products 95
4.4 Direct benefits to the plant 104
4.5 Indirect benefits to the plant 107
4.6 Challenges in understanding the mode of action 107
4.7 Future perspectives and conclusion 108
References 109

5. Role of AM fungi in growth promotion of

high-value crops 121
Manoj Parihar, Manoj Kumar Chitara, Hanuman Ram,
Asha Kumari, Gopal Tiwari, Kiran Rana, Bisweswar Gorain,
Utkarsh Kumar, Jaideep Kumar Bisht, Lakshmi Kant
5.1 Introduction 121
5.2 Arbuscular mycorrhizal fungi 122
5.3 AMF mediated benefits to high-value crops 123
5.4 AMF application in micro propagation programme 128
5.5 Commercialization of AM fungi 128
5.6 Challenges of AMF technology 134
5.7 Conclusion and future prospects 135
References 136
 Contents vii

6. Pseudomonas and Bacillus: A biological tool for

crop protection 145
A. Muthukumar, T. Suthin Raj, S.R. Prabhukarthikeyan,
R. Naveen Kumar, U. Keerthana
6.1 Introduction 145
6.2 Pseudomonas 146
6.3 Bio-control activity of Pseudomonas against plant pathogens 149
6.4 Bio-control activity of Bacillus spp. against plant pathogens 152
References 153

7. Underlying forces of plant microbiome and their effect

on plant development 159
Ankita Singh, Akash Hidangmayum, Bhudeo Rana Yashu,
Vivek Kumar, Bansh Narayan Singh, Padmanabh Dwivedi
7.1 Introduction 159
7.2 Plant microbiome diversity 160
7.3 Dynamic of plant microbes in plants 162
7.4 Plant microbe’s adaptability 163
7.5 Microbiome functions 165
7.6 Conclusions and future prospects 171
References 172

8. Plant viruses as biopesticides 181

Avinash Marwal, Akhilesh Kumar Srivastava, R.K. Gaur
8.1 Introduction 181
8.2 Research methodology 182
8.3 Categories of pesticides 182
8.4 Major viral biopesticides 182
8.5 Mode of action 183
8.6 Formulation / synthesis of viral biopesticides 184
8.7 Biopesticides manufacturing companies 185
8.8 Governing authorities / policies 186
8.9 RNAi viral biopesticides with nanotech approach 186
viii Contents

8.10 Recombinant viral biopesticides 187

8.11 A case study 187
8.12 Challenges and drawbacks 188
8.13 Major advantages 188
8.14 Conclusion, future prospects and take away 189
Acknowledgment 189
References 189

9. Microalgal based biostimulants as alleviator of biotic

and abiotic stresses in crop plants 195
Sumit Kumar, Tulasi Korra, U.B. Singh, Shailendra Singh,
Kartikay Bisen
9.1 Introduction 195
9.2 Positive effects of microalgal extract on plant growth and
productivity 202
9.3 Microalgal biostimulants for managements of biotic and
abiotic stress 204
9.4 Microalgal biostimulants emphasized under abiotic stress 205
9.5 Effects of microalgae biostimulants on biotic stress 206
9.6 Microalgal extract: a mixture with multifaceted
mechanisms 207
9.7 Concluding remarks and future prospects 210
References 211

10. Utilization of omics approaches for underpinning

plant-microbe interaction 217
Manmeet Kaur, Ravneet Kaur, H.S. Sodhi
10.1 Introduction 217
10.2 Plant- microbial communications 218
10.3 Rhizospheric root microbial interaction 218
10.4 Endosphere and microbial communication 219
10.5 Plant microbial interaction and quorum sensing 220
 Contents ix

10.6 Fungal-plant interaction 220

10.7 Plant-microbe signaling 222
10.8 Agrobacterium – crown gall disease 222
10.9 Different perspectives of bioinformatics to apprehend
soil microorganisms 223
10.10 Plant-microbe interactions promote plant growth 223
10.11 Omics approaches for plant-microbe interaction 226
10.12 Transcriptomics 226
10.13 Next generation sequencing 227
10.14 Amplicon sequencing 228
10.15 Reverse transcription polymerase chain reaction (RT-PCR)
and real-time polymerase chain reaction (qPCR) 228
10.16 TRAC anaylsis 229
10.17 Biochemical methods 229
10.18 Laser microdisinfection 230
10.19 CRISPR 230
10.20 Proteomics 231
10.21 Two- dimensional gel electrophoresis (2-DE) 231
10.22 Fluorescence 2-D difference gel electrophoresis (DIGE) 232
10.23 Isotope-Coded affinity tag (ICAT) 232
10.24 Mass spectrometry 233
10.25 Secretome 233
10.26 Metagenomics 234
10.27 Conclusion and future prospect 235
References 235

11. Extremophiles for sustainable agriculture 243

Archana S. Rao, Ajay Nair, Veena S. More, K.S Anantharaju, Sunil S. More
11.1 Introduction 243
11.2 Temperature 244
11.3 Thermophiles in agriculture 244
x Contents

11.4 Psychrophiles in agriculture 245

11.5 Ice-binding proteins 246
11.6 Anti-freeze proteins (AFPs) 247
11.7 pH tolerants in agriculture 247
11.8 Alkalophiles and acidophiles in relation to soil pH 248
11.9 Managing high and low pH stressors in plants 248
11.10 PGPM enhanced tolerance to soil acidity 248
11.11 PGPM enhanced tolerance to soil alkalinity 249
11.12 Drought resistance 249
11.13 Halophiles in agriculture 251
11.14 Radiations 254
11.15 Managing toxins and chemicals in soil 255
11.16 Biosurfactants 256
11.17 Future perspectives 257
References 258

12. Seed biopriming with biopesticide: A key to

sustainability of agriculture 265
Sananda Mondal, Debasish Panda, Bandana Bose
12.1 Introduction 265
12.2 Agricultural sustainability 265
12.3 Biopesticides 268
12.4 Biopriming with beneficial microbes 270
12.5 Seed priming and its mechanism of action 271
12.6 Biopriming and induced systemic resistance 272
12.7 Biopriming and sustainable agriculture 277
12.8 Conclusion 280
References 281

13. Insights into novel cell immobilized microbial inoculants 289

Sharon Nagpal, K.C. Kumawat, Poonam Sharma
13.1 Introduction 289
13.2 Bio-inoculant formulations and challenges 290
 Contents xi

13.3 Contemporary vs advanced formulations 291

13.4 Microbial immobilization 291
13.5 Advanced bio-encapsulation 295
13.6 Carriers used in bio-encapsulation 300
13.7 Additives in immobilization matrix 302
13.8 Microbial exo-polysaccharides- the miracle molecules 305
13.9 Cell immobilization, microbial biomass and physiology 306
13.10 Microbial resilience in immobilized cells 307
13.11 Immobilized microbial cells in agriculture 308
13.12 Immobilized microbes as bio-remediators 309
13.13 Conclusion and future prospective 310
References 311

14. Role of mycorrhizosphere as a biostimulant and its

impact on plant growth, nutrient uptake and stress
management 319
P. Sakthieaswari, Aarthy Kannan, S. Baby
14.1 Introduction 319
14.2 Plant growth promoting rhizobacteria (PGPR) 320
14.3 Plant health promoting fungi (PGPF) 322
14.4 Biostimulant phenomenon of mycorrhizosphere for
sustainable agriculture 322
14.5 Efficiency of nutrient uptake 323
14.6 Mycorrhizospheric effect on stress management 325
14.7 Symbiotic effect of arbuscular mycorrhizae 327
14.8 Effect of AM fungi on mycorrhizosphere bacteria
and vice versa 328
14.9 Significance of AM fungi on enhancing sustainable
plant growth 328
14.10 Conclusion 331
14.11 Future prospects 331
References 331
xii Contents

15. Trichoderma spp. as bio-stimulant: Molecular insights 337

Efath Shahnaz, Ali Anwar, Saba Banday
15.1 Introduction 337
15.2 Hormones 339
15.3 Volatile organic compounds 340
15.4 Other secondary metabolites 340
15.5 Bioaugmentation and biostimulation of problem soils 341
15.6 Efficacy of microbial bio-stimulation 342
15.7 Synergistic actions 342
15.8 Formulations 343
15.9 Conclusions and future prospects 343
References 344

16. Enhancing the growth and disease suppression ability

of Pseudomonas fluorescens 351
R.M. Gade, Mina D. Koche
16.1 Introduction 351
16.2 Mechanism of biocontrol by Pseudomonas 352
16.3 Plant growth promotions 355
16.4 Molecular confirmations of Pseudomonas fluorescens
by 16S ribosomal RNA sequencing 356
16.5 Control of plant diseases in crops 356
16.6 Future prospects and conclusion 361
References 361

17. Synthetic biology tools: Engineering microbes for

biotechnological applications 369
Vanshika Goyal, Isha Kohli, Vivek Ambastha, Priyanka Das, Prashant
Kumar Singh, Ajit Varma, Rachna Pandey, Naveen Chandra Joshi
17.1 Introduction 369
17.2 History of synthetic biology 370
17.3 Engineering central dogma of life 371
 Contents xiii

17.4 Designing of synthetic biology tools 375

17.5 Build-up of synthetic biology tools 380
17.6 Testing of DNA constructs 383
17.7 Application of synthetic biological tools 385
17.8 Challenges in the way of synthetic biology tools 388
17.9 Conclusion 390
References 390

18. Role of microbial consortia in remediation of soil, water

and environmental pollution caused by indiscriminate
use of chemicals in agriculture: Opportunities and
challenges 399
Lopamudra Behera, Diptanu Datta, Sunil Kumar, Sumit Kumar,
Bana Sravani, Ram Chandra
18.1 Introduction 399
18.2 Microbial consortia 400
18.3 Soil, water and environmental pollution and
bioremediation by microbial consortia 403
18.4 Future opportunities and challenges 411
18.5 Concluding remarks 412
References 412

19. Sustainable agriculture and viral diseases of plants:

An overview 419
Gajendra Mohan Baldodiya, Richita Saikia, Ricky Raj Paswan,
Basanta Kumar Borah
19.1 Introduction 419
19.2 Plant stress and immune response 421
19.3 Biostimulants 424
19.4 Sustainable agriculture, biotechnology and plant viruses 425
19.5 Conclusion 427
References 430
xiv Contents

20. Enhancement of plant nutrient uptake by bacterial

biostimulants 435
Shalja Verma, Anand Kumar Pandey
20.1 Introduction 435
20.2 Plant nutrient uptake mechanisms 437
20.3 Biostimulants 438
20.4 Categories of biostimulants and their effect on plant
growth and productivity 439
20.5 Indirect mechanism of bacterial biostimulants to
enhance nutrient uptake 445
20.6 Direct mechanism of bacterial biostimulants to enhance
plant nutrient uptake 447
20.7 Bacterial biostimulants to enhance the growth and
stress tolerance 448
20.8 Bacterial biostimulants as biocontrol agents 449
20.9 Conclusion and prospects 450
References 450

Index  457
Contributors

S. Abirami CEOA Matriculation Higher Secondary School, Madurai, Tamil Nadu, India

Muhammad Faheem Adil Department of Agronomy, College of Agriculture and

Biotechnology, Key Laboratory of Crop Germplasm Resource, Zhejiang University,
Hangzhou, China

Nishar Akhtar Department of Plant Pathology, Birsa Agricultural University, Ranchi,

Bihar, India

Khizer Amanet Department of Environmental Sciences, COMSATS University

Islamabad, Vehari Campus, Pakistan

Vivek Ambastha Department of Plant Sciences, Migal Galilee Research Institute, Israel

K.S Anantharaju Department of Chemistry, Dayananda Sagar Collge of Engineering,

Bangalore, Karnataka, India

Julieta A. Anarna National Institute of Molecular Biology and Biotechnology University

of the Philippines, Los Banos (BIOTECH-UPLB)

Ali Anwar Division of Plant Pathology, Faculty of Horticulture, Sher-e-Kashmir

University of Agricultural Sciences & Technology-Kashmir, Shalimar Campus, Srinagar,
Jammu & Kashmir, India

Habib-ur-Rehman Athar Institute of Pure and Applied Biology, Bahauddin Zakariya

University, Multan, Pakistan

S. Baby HS Biology faculty, Narayana e-techno School, Madurai, Tamil Nadu, India

Gajendra Mohan Baldodiya School of Biological Sciences, UM-DAE Centre for

Excellence in Basic Science, Mumbai University, Kalina Campus, Santacruz (East),
Mumbai, Maharashtra, India

Saba Banday Division of Plant Pathology, Faculty of Horticulture, Sher-e-Kashmir

University of Agricultural Sciences & Technology-Kashmir, Shalimar Campus, Srinagar,
Jammu & Kashmir, India

Lopamudra Behera Department of Mycology and Plant Pathology, Institute of

Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India

Kartikay Bisen Faculty of Agricultural Sciences and Allied Industries, Rama University,
Kanpur, Uttar Pradesh, India
xv
xvi Contributors

Jaideep Kumar Bisht ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan

(VPKAS), Almora, Uttarakhand, India
Basanta Kumar Borah Department of Agricultural Biotechnology, Assam Agricultural
University, Jorhat, Assam, India
Bandana Bose Department of Plant Physiology, Institute of Agricultural Sciences,
Banaras Hindu University, Varanasi, Uttar Pradesh, India
Cristine Marie B. Brown National Institute of Molecular Biology and Biotechnology
University of the Philippines, Los Banos (BIOTECH-UPLB)
Marilyn B. Brown National Institute of Molecular Biology and Biotechnology University
of the Philippines, Los Banos (BIOTECH-UPLB)
Ram Chandra Department of Mycology and Plant Pathology, Institute of Agricultural
Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
Manoj Kumar Chitara Department of Plant Pathology, College of Agriculture, GBPUAT,
Panatnagar, Uttarakhand, India
Arzu Çiğ Department of Horticulture, Siirt University, Siirt, Turkey
Subhan Danish Department of Soil Science, Faculty of Agricultural Sciences and
Technology, Bahauddin Zakariya University, Multan, Pakistan
Priyanka Das Division of Plant Biology, Bose Institute, Kolkata, West Bengal, India
Diptanu Datta Department of Plant Pathology, College of Agriculture, Odisha
University of Agriculture and Technology, Bhubaneswar, Odisha, India
Padmanabh Dwivedi Department of Plant Physiology, Institute of Agricultural
Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
Murat Erman Department of Field Crops, Faculty of Agriculture, Siirt University, Turkey
R.M. Gade Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra, India
R.K. Gaur Department of Biotechnology, DeenDayal Upadhyaya Gorakhpur University,
Gorakhpur, Uttar Pradesh, India
Bisweswar Gorain ICAR-CSSRI, RRS Bharuch, Gujarat, India
Vanshika Goyal Amity Institute of Microbial Technology, Amity University, Noida,
Uttar Pradesh, India
Akash Hidangmayum Department of Plant Physiology, Institute of Agricultural
Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
Akbar Hossain Bangladesh Wheat and Maize Research Institute, Dinajpur, Bangladesh
Muhammad Imran University of Poonch Rawalakot, Department of Entomology,
Rawalakot, Pakistan
 Contributors xvii

Muhammad Aamir Iqbal University of Poonch Rawalakot, Department of Agronomy,

Rawalakot, Pakistan
Md. Sohidul Islam Department of Agronomy, Hajee Mohammad Danesh Science and
Technology University, Dinajpur, Bangladesh
Naveen Chandra Joshi Amity Institute of Microbial Technology, Amity University,
Noida, Uttar Pradesh, India
Aarthy Kannan HS Biology faculty, Narayana e-techno School, Madurai, Tamil Nadu,
India
Lakshmi Kant ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan (VPKAS),
Almora, Uttarakhand, India
Manmeet Kaur Department of Microbiology, Punjab Agricultural University, Ludhiana,
Punjab, India
Ravneet Kaur Department of Microbiology, Punjab Agricultural University, Ludhiana,
Punjab, India
U. Keerthana Crop Protection Division, ICAR-National Rice Research Institute, Cuttack,
Odisha, India
Mina D. Koche Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra, India
Isha Kohli Amity Institute of Microbial Technology, Amity University, Noida,
Uttar Pradesh, India
Tulasi Korra Department of Mycology and Plant Pathology, Institute of Agricultural
Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
Singh Kulvir Punjab Agricultural University, Regional Research Station, Faridkot,
Punjab, India
Gagan Kumar Department of Plant Pathology, M. S. Swaminathan School of
Agriculture, Centurion University of Technology and Management, Odisha, India
Utkarsh Kumar ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan (VPKAS),
Almora, Uttarakhand, India
Vivek Kumar Department of Plant Physiology, Institute of Agricultural Sciences,
Banaras Hindu University, Varanasi, Uttar Pradesh, India
Sumit Kumar Department of Mycology and Plant Pathology, Institute of Agricultural
Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
Sunil Kumar Plant Protection, International Rice Research Institute (IRRI), Bhubaneswar,
Odisha, India
Asha Kumari ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan (VPKAS),
Almora, Uttarakhand, India
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